#include <Extender.hh>

Inheritance diagram for protocols::star::Extender:

Public Member Functions
	Extender (core::sequence::SequenceAlignmentCOP alignment, int num_residues)

void	extend_unaligned (core::pose::Pose *pose)

protocols::loops::LoopsCOP	unaligned () const
	Returns the unaligned regions in increasing order of start position. More...

protocols::loops::LoopsCOP	aligned () const
	Returns the aligned regions in increasing order of start position. More...

const utility::vector1< int > &	cutpoints () const
	Returns a set of suggested cutpoints for star fold tree construction based on information gathered during extend_unaligned(). More...

void	set_secondary_structure (core::fragment::SecondaryStructureCOP pred_ss)
	Updates predicted secondary structure, improving cutpoint selection. More...

Protected Member Functions
int	choose_cutpoint (int start, int stop) const

Private Attributes
core::sequence::SequenceAlignmentCOP	alignment_

protocols::loops::LoopsOP	unaligned_

protocols::loops::LoopsOP	aligned_

core::fragment::SecondaryStructureCOP	pred_ss_

utility::vector1< int >	cutpoints_

Constructor & Destructor Documentation

protocols::star::Extender::Extender	(	core::sequence::SequenceAlignmentCOP	alignment,
		int	num_residues
	)

References aligned_, protocols::comparative_modeling::pick_loops_unaligned(), and unaligned_.

Member Function Documentation

protocols::loops::LoopsCOP protocols::star::Extender::aligned ( ) const

inline

Returns the aligned regions in increasing order of start position.

References aligned_.

int protocols::star::Extender::choose_cutpoint	(	int	start,
		int	stop
	)		const

protected

Selects a cutpoint on the closed interval [start, stop] using weighted reservoir sampling. Each residue's weight is proportional to its likelihood of being a loop.

References pred_ss_, and protocols::loops::stop.

Referenced by extend_unaligned().

const utility::vector1<int>& protocols::star::Extender::cutpoints ( ) const

inline

Returns a set of suggested cutpoints for star fold tree construction based on information gathered during extend_unaligned().

References cutpoints_.

void protocols::star::Extender::extend_unaligned ( core::pose::Pose * pose )

Sets unaligned residues' torsion angles to their extended values and idealizes bond lengths and angles. The placement of unaligned residues depends on the number of residues separating the adjacent aligned regions.

Given aligned regions a_1 and a_2 with (a_1.start < a_2.start):

If (a_2.start - a_1.stop) <= -abinitio:star:short_loop_len, the unaligned residues are grown off a_1.stop. Otherwise, a stochastically selected portion of the residues are grown off a_1.stop and the remainder grown off a_2.start. In both cases, the method is responsible for noting the interior cutpoints it selected.

References core::kinematics::FoldTree::add_edge(), aligned_, core::scoring::calpha_superimpose_pose(), choose_cutpoint(), core::pose::Pose::conformation(), protocols::star::copy_residues(), cutpoints_, core::pose::Pose::fold_tree(), protocols::star::generate_extended_pose(), core::conformation::idealize_position(), core::kinematics::Edge::PEPTIDE, core::pose::Pose::sequence(), core::pose::Pose::size(), protocols::loops::Loop::start(), and protocols::loops::Loop::stop().